[Debian-med-packaging] Bug#905706: Bug#905706: libpicard-java-doc: ships /usr/share/javascript/jquery/jquery.min.js

Tue Sep 18 09:38:31 BST 2018


On 09/18/2018 10:02 AM, Olivier Sallou wrote:
>
> On 09/17/2018 04:36 PM, Andreas Tille wrote:
>> Control: tags -1 pending
>>
>> This issue should be fixed in
>>    https://salsa.debian.org/med-team/picard-tools/commit/4da851972983cee93a3cce27bfbb40f9648dcc3d
>>
>>
>> While fixing the bug I also tried to upgrade the package to the latest upstream
>> version.  Unfortunately this failed with:
>>
>>
>> Compiling build file '/build/picard-tools-2.18.14+dfsg/build.gradle' using BuildScriptTransformer.
>>         Adding Maven pom generation to project 'picard'
>>         Linking the generated javadoc to the system JDK API documentation
>>
>> FAILURE: Build failed with an exception.
>>
>> * Where:
>> Build file '/build/picard-tools-2.18.14+dfsg/build.gradle' line: 53
I have fixed the build issue, and pushed updates in git.
build was tested against latest htsjdk 2.16.1 (not yet pushed to sid)
>>
>> * What went wrong:
>> A problem occurred evaluating root project 'picard'.
>>> The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK must be installed. See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard
> I fixed the issue and could compile, however there is one test failing
> for the moment.
> I gonna investiguate and push my updates afterwards.
>
> Olivier
>> * Try:
>> Run with --debug option to get more log output.
>>
>> * Exception is:
>> org.gradle.api.GradleScriptException: A problem occurred evaluating root project 'picard'.
>>         at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:92)
>>         at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl$2.run(DefaultScriptPluginFactory.java:176)
>>         at org.gradle.configuration.ProjectScriptTarget.addConfiguration(ProjectScriptTarget.java:77)
>>         at org.gradle.configuration.DefaultScriptPluginFactory$ScriptPluginImpl.apply(DefaultScriptPluginFactory.java:181)
>>         at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:39)
>>         at org.gradle.configuration.project.BuildScriptProcessor.execute(BuildScriptProcessor.java:26)
>>         at org.gradle.configuration.project.ConfigureActionsProjectEvaluator.evaluate(ConfigureActionsProjectEvaluator.java:34)
>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.doConfigure(LifecycleProjectEvaluator.java:70)
>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.access$000(LifecycleProjectEvaluator.java:33)
>>         at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:53)
>>         at org.gradle.configuration.project.LifecycleProjectEvaluator$1.execute(LifecycleProjectEvaluator.java:50)
>>         at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:61)
>>         at org.gradle.configuration.project.LifecycleProjectEvaluator.evaluate(LifecycleProjectEvaluator.java:50)
>>         at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:599)
>>         at org.gradle.api.internal.project.DefaultProject.evaluate(DefaultProject.java:125)
>>         at org.gradle.execution.TaskPathProjectEvaluator.configure(TaskPathProjectEvaluator.java:35)
>>         at org.gradle.execution.TaskPathProjectEvaluator.configureHierarchy(TaskPathProjectEvaluator.java:60)
>>         at org.gradle.configuration.DefaultBuildConfigurer.configure(DefaultBuildConfigurer.java:38)
>>         at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:233)
>>         at org.gradle.initialization.DefaultGradleLauncher$ConfigureBuildAction.execute(DefaultGradleLauncher.java:230)
>>         at org.gradle.internal.Transformers$4.transform(Transformers.java:169)
>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:106)
>>         at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:56)
>>         at org.gradle.initialization.DefaultGradleLauncher.doBuildStages(DefaultGradleLauncher.java:160)
>>         at org.gradle.initialization.DefaultGradleLauncher.doBuild(DefaultGradleLauncher.java:119)
>>         at org.gradle.initialization.DefaultGradleLauncher.run(DefaultGradleLauncher.java:102)
>>         at org.gradle.launcher.exec.GradleBuildController.run(GradleBuildController.java:71)
>>         at org.gradle.tooling.internal.provider.ExecuteBuildActionRunner.run(ExecuteBuildActionRunner.java:28)
>>         at org.gradle.launcher.exec.ChainingBuildActionRunner.run(ChainingBuildActionRunner.java:35)
>>         at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:41)
>>         at org.gradle.launcher.exec.InProcessBuildActionExecuter.execute(InProcessBuildActionExecuter.java:26)
>>         at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:75)
>>         at org.gradle.tooling.internal.provider.ContinuousBuildActionExecuter.execute(ContinuousBuildActionExecuter.java:49)
>>         at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:49)
>>         at org.gradle.tooling.internal.provider.ServicesSetupBuildActionExecuter.execute(ServicesSetupBuildActionExecuter.java:31)
>>         at org.gradle.launcher.daemon.server.exec.ExecuteBuild.doBuild(ExecuteBuild.java:67)
>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.WatchForDisconnection.execute(WatchForDisconnection.java:47)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.ResetDeprecationLogger.execute(ResetDeprecationLogger.java:26)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.RequestStopIfSingleUsedDaemon.execute(RequestStopIfSingleUsedDaemon.java:34)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:74)
>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput$2.call(ForwardClientInput.java:72)
>>         at org.gradle.util.Swapper.swap(Swapper.java:38)
>>         at org.gradle.launcher.daemon.server.exec.ForwardClientInput.execute(ForwardClientInput.java:72)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.LogAndCheckHealth.execute(LogAndCheckHealth.java:50)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.LogToClient.doBuild(LogToClient.java:60)
>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.EstablishBuildEnvironment.doBuild(EstablishBuildEnvironment.java:72)
>>         at org.gradle.launcher.daemon.server.exec.BuildCommandOnly.execute(BuildCommandOnly.java:36)
>>         at org.gradle.launcher.daemon.server.api.DaemonCommandExecution.proceed(DaemonCommandExecution.java:120)
>>         at org.gradle.launcher.daemon.server.exec.StartBuildOrRespondWithBusy$1.run(StartBuildOrRespondWithBusy.java:50)
>>         at org.gradle.launcher.daemon.server.DaemonStateCoordinator$1.run(DaemonStateCoordinator.java:297)
>>         at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>         at org.gradle.internal.concurrent.StoppableExecutorImpl$1.run(StoppableExecutorImpl.java:46)
>> Caused by: org.gradle.api.GradleException: The ClassLoader obtained from the Java ToolProvider is null. A Java 8 JDK must be installed. See https://github.com/broadinstitute/picard/blob/master/README.md#building-picard for information on how to build picard
>>         at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>>         at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>         at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>>         at build_e2g2wljk0xfne1q452c0qhi2d.ensureBuildPrerequisites(/build/picard-tools-2.18.14+dfsg/build.gradle:53)
>>         at build_e2g2wljk0xfne1q452c0qhi2d$ensureBuildPrerequisites.callCurrent(Unknown Source)
>>         at build_e2g2wljk0xfne1q452c0qhi2d.run(/build/picard-tools-2.18.14+dfsg/build.gradle:61)
>>         at org.gradle.groovy.scripts.internal.DefaultScriptRunnerFactory$ScriptRunnerImpl.run(DefaultScriptRunnerFactory.java:90)
>>         ... 62 more
>>
>>
>> BUILD FAILED
>>
>> Total time: 6.725 secs
>>
>>
>>
>> Could any of the more skilled Java developers of the team please have a look?
>>
>> Kind regards
>>
>>      Andreas.
>>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438